MRC Transition Support CSF Nicholas Matheson
Lead Research Organisation:
University of Cambridge
Department Name: Medicine
Abstract
Approximately 100 years since it was first transmitted to humans, the Human Immunodeficiency Virus (HIV) infects almost 40 million people worldwide, and causes around 1 million AIDS-related deaths every year. It is therefore critical to understand how HIV has been able to replicate and spread, and why HIV infection causes AIDS. "Proteomics" is the large-scale study of "proteins", the critical building blocks of living cells and organisms. I previously used proteomics to measure changes in the number and quantity of proteins at the surface of cells infected with HIV, and identified many proteins specifically depleted by the virus.
Proteins are themselves made up of long chains of "amino acids", and many of the proteins I found to be depleted by HIV are involved in transporting amino acids into cells. These "amino acid transporters" are relatively understudied, and may be attractive candidates for new drugs. I therefore wish to understand why amino acid transporters are targeted by HIV, and the importance of these transporters for "helper T cells", the main cells of the immune system infected by HIV and progressively destroyed in patients with AIDS.
Amongst the HIV targets I identified were proteins called SNAT1 and SERINC3/5. I discovered that SNAT1 transports an amino acid called alanine into cells, and that an abundant supply of alanine is essential for normal helper T cell function. Likewise, SERINC proteins are thought to incorporate an amino acid called serine into "cell membranes", which surround cells and separate their interiors into compartments.
During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a new way of purifying HIV-infected helper T cells; perfected a way to extract amino acids and other "metabolites" from these cells; and developed a transformative approach to measuring transport of amino acids in and out of cells. I therefore now wish to use these techniques to figure out which metabolic processes in cells are manipulated by HIV, and why they are important for the HIV virus and helper T cells.
In particular, they will enable me to: measure amino acid transport by SNAT1 and SERINC3/5 in growing cells; map global changes in metabolites and metabolism in HIV-infected primary CD4+ T cells; and characterise other critical amino acid transporters of helper T cells identified using different, unrelated approaches earlier in my fellowship. Taken together, these data will be a valuable resource for other researchers in the field and will, I hope, ultimately lead to the development of new treatments for patients targeting amino acid transporters in T cells.
Proteins are themselves made up of long chains of "amino acids", and many of the proteins I found to be depleted by HIV are involved in transporting amino acids into cells. These "amino acid transporters" are relatively understudied, and may be attractive candidates for new drugs. I therefore wish to understand why amino acid transporters are targeted by HIV, and the importance of these transporters for "helper T cells", the main cells of the immune system infected by HIV and progressively destroyed in patients with AIDS.
Amongst the HIV targets I identified were proteins called SNAT1 and SERINC3/5. I discovered that SNAT1 transports an amino acid called alanine into cells, and that an abundant supply of alanine is essential for normal helper T cell function. Likewise, SERINC proteins are thought to incorporate an amino acid called serine into "cell membranes", which surround cells and separate their interiors into compartments.
During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a new way of purifying HIV-infected helper T cells; perfected a way to extract amino acids and other "metabolites" from these cells; and developed a transformative approach to measuring transport of amino acids in and out of cells. I therefore now wish to use these techniques to figure out which metabolic processes in cells are manipulated by HIV, and why they are important for the HIV virus and helper T cells.
In particular, they will enable me to: measure amino acid transport by SNAT1 and SERINC3/5 in growing cells; map global changes in metabolites and metabolism in HIV-infected primary CD4+ T cells; and characterise other critical amino acid transporters of helper T cells identified using different, unrelated approaches earlier in my fellowship. Taken together, these data will be a valuable resource for other researchers in the field and will, I hope, ultimately lead to the development of new treatments for patients targeting amino acid transporters in T cells.
Technical Summary
Approximately 100 years since its transmission to humans, HIV-1 infects almost 40 million people worldwide, and causes around 1 million AIDS-related deaths every year. I previously used TMT-based plasma membrane proteomics to gain a comprehensive, unbiased overview of cell surface proteins regulated by HIV infection. In addition to known targets, I discovered HIV-mediated downregulation of the amino acid transporter SNAT1, and the putative serine carriers SERINC3/5.
I found SNAT1 to be dramatically upregulated at the surface of activated T cells, identified alanine as an endogenous SNAT1 substrate, and showed that extracellular alanine is essential for T cell mitogenesis. Along with SNAT1 and SERINC3/5, I also observed regulation of other transmembrane transporters, suggesting a general paradigm for HIV-mediated manipulation of nutrient uptake and cellular metabolism.
During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a reporter virus (HIV-AFMACS) allowing magnetic selection of HIV-infected primary CD4+ T cells; optimised a novel method for metabolite extraction from these cells; and developed a transformative stable isotope-based approach to quantitate amino acid transport.
I therefore now wish to leverage these techniques to further elucidate the metabolic processes manipulated by HIV, and define their importance in HIV pathogenesis and T cell immunobiology. In particular, they will enable me to: quantitate amino acid transport by SNAT1 and SERINC3/5 under normal growth conditions in a comprehensive, unbiased fashion; map global metabolic changes in HIV-infected primary CD4+ T cells; and characterise other critical mitogenic amino acid transporters of CD4+ T cells identified by a combined proteomic-genetic screening approach.
I found SNAT1 to be dramatically upregulated at the surface of activated T cells, identified alanine as an endogenous SNAT1 substrate, and showed that extracellular alanine is essential for T cell mitogenesis. Along with SNAT1 and SERINC3/5, I also observed regulation of other transmembrane transporters, suggesting a general paradigm for HIV-mediated manipulation of nutrient uptake and cellular metabolism.
During the first 2.5 years of my Clinician Scientist Fellowship, I have: developed a reporter virus (HIV-AFMACS) allowing magnetic selection of HIV-infected primary CD4+ T cells; optimised a novel method for metabolite extraction from these cells; and developed a transformative stable isotope-based approach to quantitate amino acid transport.
I therefore now wish to leverage these techniques to further elucidate the metabolic processes manipulated by HIV, and define their importance in HIV pathogenesis and T cell immunobiology. In particular, they will enable me to: quantitate amino acid transport by SNAT1 and SERINC3/5 under normal growth conditions in a comprehensive, unbiased fashion; map global metabolic changes in HIV-infected primary CD4+ T cells; and characterise other critical mitogenic amino acid transporters of CD4+ T cells identified by a combined proteomic-genetic screening approach.
Planned Impact
The primary beneficiaries from my results will be other researchers in the fields of retrovirology, immunology and metabolism. I will generate a significant quantity of data that may be shared for added benefit, and will provide a useful resource for the community. To my knowledge, this body of work will represent the first systematic application of stable isotope-based tracing to quantitate amino acid transport. As such, it has the potential to transform the way scientists measure and understand transport of amino acids and other metabolites.
Critically, the novel techniques to quantitate metabolism described in this application are applicable to a wide range of cell biological questions, not just HIV/immunometabolism. I am committed to sharing detailed methods with other researchers, to enhance the efficiency and reproducibility of research in the field. Materials used during this project will also be useful to the wider community, such as the HIV-AFMACS virus. Judging by the number of requests I have previously received for AFMACS reagents, I anticipate that these molecular clones will be in high demand.
Although my proposal involves basic science rather than clinically directed research, it is focused on areas of particular relevance to human disease, with the ultimate aim to deliver novel therapeutic approaches to the clinic. Metabolic pathways targeted by HIV represent candidate targets for antiviral therapy, particularly if they are essential for viral replication but not cellular survival. More immediately, cell surface transporters are readily druggable targets, and cell type specific expression offers the opportunity for focussed immunomodulatory therapies targeting mitogenic pathways such as mTOR in CD4+ T cells.
In a wider context, my time in Matthew's Vander Heiden's laboratory at MIT has provided me with a world-class training in the study of metabolism. I am now using this as a springboard to further develop my research programme in Cambridge, including contributing to the new Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID) Immunometabolic Core facility. There is a growing interest in metabolism within the Department of Medicine and on the campus, and I anticipate that further collaborative and inter-disciplinary projects will be readily forthcoming, with beneficial cross-fertilisation of the research of other groups. I will therefore disseminate my research skills as well as data, and the first beneficiary of this will be my RA.
Critically, the novel techniques to quantitate metabolism described in this application are applicable to a wide range of cell biological questions, not just HIV/immunometabolism. I am committed to sharing detailed methods with other researchers, to enhance the efficiency and reproducibility of research in the field. Materials used during this project will also be useful to the wider community, such as the HIV-AFMACS virus. Judging by the number of requests I have previously received for AFMACS reagents, I anticipate that these molecular clones will be in high demand.
Although my proposal involves basic science rather than clinically directed research, it is focused on areas of particular relevance to human disease, with the ultimate aim to deliver novel therapeutic approaches to the clinic. Metabolic pathways targeted by HIV represent candidate targets for antiviral therapy, particularly if they are essential for viral replication but not cellular survival. More immediately, cell surface transporters are readily druggable targets, and cell type specific expression offers the opportunity for focussed immunomodulatory therapies targeting mitogenic pathways such as mTOR in CD4+ T cells.
In a wider context, my time in Matthew's Vander Heiden's laboratory at MIT has provided me with a world-class training in the study of metabolism. I am now using this as a springboard to further develop my research programme in Cambridge, including contributing to the new Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID) Immunometabolic Core facility. There is a growing interest in metabolism within the Department of Medicine and on the campus, and I anticipate that further collaborative and inter-disciplinary projects will be readily forthcoming, with beneficial cross-fertilisation of the research of other groups. I will therefore disseminate my research skills as well as data, and the first beneficiary of this will be my RA.
Publications
Abbott K
(2023)
Screening in serum-derived medium reveals differential response to compounds targeting metabolism
in Cell Chemical Biology
Gerber P
(2022)
XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection
Gerber PP
(2022)
XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection.
in Nature communications
Jackson H
(2024)
Bioengineered small extracellular vesicles deliver multiple SARS-CoV-2 antigenic fragments and drive a broad immunological response
in Journal of Extracellular Vesicles
Krishna B
(2024)
Spontaneous, persistent, T cell-dependent IFN-? release in patients who progress to Long Covid
in Science Advances
Description | Membership of NIHR Cambridge BioResource Scientific Advisory Board Membership |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Participation in a guidance/advisory committee |
URL | https://bioresource.nihr.ac.uk/centres-programmes/bioresource-centre-cambridge/ |
Description | Engineered SARS-CoV-2 for rapid live virus neutralising antibody assays |
Amount | £36,255 (GBP) |
Funding ID | PATH 01 |
Organisation | NHS Blood and Transplant (NHSBT) |
Sector | Public |
Country | United Kingdom |
Start | 09/2023 |
End | 03/2025 |
Description | Institutional Strategic Support Fund - Regulation of T cell amino acid tranpsort by the tumour microenvironment |
Amount | £56,267 (GBP) |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2021 |
End | 03/2023 |
Description | Multiscale analysis of HIV-1-induced small T cell syncytia |
Amount | $2,703,932 (USD) |
Funding ID | R01AI172486 |
Organisation | National Institutes of Health (NIH) |
Sector | Public |
Country | United States |
Start | 07/2023 |
End | 07/2028 |
Description | Reserach Grant - Cell-based assays for COVID-19 therapeutics |
Amount | £17,188 (GBP) |
Funding ID | #900239 |
Organisation | Addenbrooke's Charitable Trust (ACT) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2021 |
End | 06/2022 |
Description | Reserach Grant - INTEGRA ASSIST PLUS pipetting robot for high-throughput assays of neutralising antibodies against SARS-CoV-2 |
Amount | £18,870 (GBP) |
Funding ID | 900342 |
Organisation | Addenbrooke's Charitable Trust (ACT) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2022 |
End | 03/2023 |
Description | SARS COV2 vaccine ResPonse In Obesity - SCORPIO study |
Amount | £752,294 (GBP) |
Funding ID | MR/W020564/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2021 |
End | 08/2023 |
Description | Small Research Grant - Protection against SARS-CoV-2 infection by neutralising antibodies (a nested case-control study) |
Amount | £43,628 (GBP) |
Funding ID | 119PATH23 |
Organisation | NHS Blood and Transplant (NHSBT) |
Sector | Public |
Country | United Kingdom |
Start | 09/2022 |
End | 09/2024 |
Description | Small Reserach Project Grant - Regulation of HIV replication by virion-associated RNA helicases |
Amount | £20,000 (GBP) |
Organisation | British Infection Association (BIA) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 12/2021 |
End | 06/2023 |
Description | The role of SARS-CoV-2 Nucleocapsid mutations in COVID-19 disease |
Amount | £38,976 (GBP) |
Funding ID | REI/1/4943 |
Organisation | King Abdullah University of Science and Technology (KAUST) |
Sector | Academic/University |
Country | Saudi Arabia |
Start | 08/2023 |
End | 08/2024 |
Description | The use of convalescent plasma to treat hospitalised and critically ill patients with COVID-19 disease |
Amount | £3,127,919 (GBP) |
Funding ID | COVID-19-RECPLAS |
Organisation | National Institute for Health Research |
Sector | Public |
Country | United Kingdom |
Start | 04/2020 |
End | 04/2023 |
Title | Luminescent reporter cell line for authentic SARS-CoV-2 infection |
Description | During the pandemic, I have applied my knowledge and skills in molecular virology to understanding and combating COVID-19. In particular, my lab has developed luminescent 'reporter cells', which emit light when they are infected with SARS-CoV-2. These allow us to test antiviral drugs, and measure 'neutralising antibodies' in blood samples from patients. We have made them available to the research community via the National Institute for Biological Standards and Control (NIBSC), catalogue number 101062, and the National Institute of Allergy and Infectious Diseases (NIAID)/BEI Resources, catalog no. NR-58714. This work has contributed to >10 collaborative research projects within the Department of Medicine, with other groups at the University of Cambridge, and with external collaborators. Across these collaborations, we have already tested >1,500 samples (contributing so far to 8 published manuscripts, 3 manuscripts in revision or under review, and several presentations at national conferences). The continuing evolution and spread of new SARS-CoV-2 variants of concern, with increasing ability to evade the humoral immune response, has highlighted how important it is to have the capability to measure variant-specific neutralising antibodies against authentic viral isolates (such as Omicron BA.1). |
Type Of Material | Cell line |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Brevini T, Maes M, Webb GJ, Fuchs CD, Buescher G, , Matheson NJ, et al. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature. 2022. doi.org/10.1038/s41586-022-05594-0. PMID: 36470304 Touizer E, Alrubayyi A, , Matheson NJ, Morris E, Peppa D, McCoy LE. Attenuated humoral responses in HIV after SARS-CoV-2 vaccination linked to B cell defects and altered immune profiles. iScience. 2023;26(1):105862. doi: 10.1016/j.isci.2022.105862. PMID: 36590902 Shilts J, Crozier TWM, Teixeira-Silva A, , Matheson NJ, Lehner PJ, Wright GJ. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. PLoS Biol. 2023;21(2):e3001959. doi: 10.1371/journal.pbio.3001959. PMID: 36735681 Pereyra Gerber P, Donde MJ, Matheson NJ, Taylor A. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun. 2022;13(1):6716. PMID: 36385143 Pereyra Gerber P, Duncan LM, Greenwood EJD, Marelli S, Naamati A, , Matheson NJ. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection. PLoS Pathog. 2022;18(2):e1010265. doi: 10.1371/journal.ppat.1010265. PMID: 35143592 Meng B, Abdullahi A, Ferreira IATM, , Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature. 2022. doi: 10.1038/s41586-022-04474-x. PMID: 35104837 Kotagiri P, Mescia F, Rae W, Bergamaschi L, Tuong Z, , Matheson NJ, et al. B Cell Receptor Repertoire Kinetics after SARS-CoV-2 Infection and Vaccination. Cell Rep. 2022;38(7):110393. doi: 10.1016/j.celrep.2022.110393. PMID: 35143756 Bergamaschi L, Mescia F, Turner L, Hanson AL, Kotagiri P, , Matheson NJ, et al. Longitudinal analysis reveals that delayed bystander CD8+ T cell activation and early immune pathology distinguish severe COVID-19 from mild disease. Immunity. 2021;54(6):1257-75 e8. Epub 2021/05/30. doi: 10.1016/j.immuni.2021.05.010. PMID: 34051148 |
URL | https://www.nibsc.org/products/brm_product_catalogue/detail_page.aspx?catid=101062 |
Description | Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration |
Organisation | National Institute for Health Research |
Department | NIHR Cambridge Biomedical Research Centre |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | I am one of the Principal Investigators contributng to the CITIID-NIHR COVID-19 BioResource Collaboration, led by Professor Smith (CITIID) and Professory Bradley (NIHR). My lab has been particularly responsible for measuring neutralising antibody levels against SARS-CoV-2 in blood samples from patients |
Collaborator Contribution | As part of the NIHR BioResource, this collaborative project has allowed people tested in hospital for COVID-19 to participate in research by providing biological samples (such as blood, and the swab used to test for COVID-19) and answering some questions about their lifestyle and mental health. NHS staff undergoing routine screening for COVID-19 have also been asked if they would like to participate, in order to safely collect samples representing a variety of COVID-19 experiences - from those displaying none or mild symptoms to those with more severe experiences. The samples have been used to support current and future research - including on-going research to find new and faster ways to test patients and staff, understand why the virus affects people in different ways and find new ways to treat the disease |
Impact | 30 publications so far indexed on PubMed (PMIDs): 36721385, 36717723, 36451358, 36420270, 36343994, 36330526, 36065116, 36058413, 35963244, 35864233, 35864232, 35224470, 35189575, 35143756, 35104837, 34488225, 34260717, 34192737, 34051148, 33879890, 33706364, 33619509, 33545711, 33398302, 33318491, 32905045, 32838340, 32737467, 32558644, 32392129 |
Start Year | 2020 |
Description | Collaboration with Thali laboratory |
Organisation | University of Vermont |
Country | United States |
Sector | Academic/University |
PI Contribution | I have created a functional proteomic atlas of HIV infection in primary human CD4+ T-cells, in which we identified over 650 specific HIV-dependent changes, including almost 200 proteins not previously identified or known to be regulated in T cell lines |
Collaborator Contribution | Professor Thali has made key contributions to study of HIV, including the development of a novel technique allowing the magnetic selection of HIV-induced T cell syncytia. We continue to collaborate on the proteomic analysis of these syncytia |
Impact | Whitaker EE, Matheson NJ, Perlee S, Munson PB, Symeonides M, Thali M. EWI-2 Inhibits Cell-Cell Fusion at the HIV-1 Virological Presynapse. Viruses. 2019;11(12). Epub 2019/11/24. doi: 10.3390/v11121082. PMID: 31757023 |
Start Year | 2019 |
Description | Collaboration with Vander Heiden laboratory |
Organisation | Massachusetts Institute of Technology |
Department | Koch Institute |
Country | United States |
Sector | Academic/University |
PI Contribution | I was a Visiting Scientist in the Vander Heiden laboratory at the David H Koch Institute for Integrative Cancer Research (MIT) 2017-18. I learnt to apply stable isotope-based metabolite tracing and metabolic flux analysis in an interdisciplinary project aimed at understanding metabolism in HIV-infected cells. I have subsequently used these skills to set up a GCMS-based metabolomic pipeline at the University of Cambridge. We continue to collaborate on projects related to immunometabolism |
Collaborator Contribution | Professor Vander Heiden has made key contributions in the field of cancer metabolism, and is co-sponsor of my MRC Clinician Scientist Fellowship. His laboratory provided training on stable isotope-based metabolite tracing and metabolic flux analysis. We continue to collaborate on projects related to immunometabolism |
Impact | Luengo A, Li Z, Gui DY, Sullivan LB, Zagorulya M, Do BT, Ferreira R... Matheson NJ, Vander Heiden MG. (2020). Increased demand for NAD relative to ATP drives aerobic glycolysis. Mol Cell. 2021 Feb 18;81(4):691-707.e6. doi: 10.1016/j.molcel.2020.12.012 Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V... Matheson NJ, Yilmaz O, Vander Heiden MG. (2020). Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma. eLife. 2020 Jul 10;9:e56782. doi: 10.7554/eLife.56782 |
Start Year | 2017 |